Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Pf1N1B4_1309 Biotin carboxylase of acetyl-CoA carboxylase (EC 6.3.4.14)
Query= BRENDA::Q42523 (734 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1309 Length = 452 Score = 406 bits (1043), Expect = e-117 Identities = 213/445 (47%), Positives = 289/445 (64%), Gaps = 5/445 (1%) Query: 38 IEKILVANRGEIACRIMRTAKRLGIQTVAVYSDADRDSLHVKSADEAVRIGPPSARLSYL 97 +EK+L+ANRGEIA RI+R K +GI+TVAVYS AD++ +H+ ADE+V IGP SA SYL Sbjct: 5 LEKVLIANRGEIALRILRACKEMGIKTVAVYSKADKELMHLGLADESVCIGPASAAHSYL 64 Query: 98 SGVTIMEAAARTGAQAIHPGYGFLSESSDFAQLCEDSGLTFIGPPASAIRDMGDKSASKR 157 I+ AA TGA AIHPGYGFL+E++DFA+ E+SG FIGP A IR MGDK ++K Sbjct: 65 HIPAIIAAAEVTGATAIHPGYGFLAENADFAEQVENSGFAFIGPKAETIRLMGDKVSAKH 124 Query: 158 IMGAAGVPLVPGYHGH-EQDIDHMKSEAEKIGYPIIIKPTHGGGGKGMRIVQSGKDFADS 216 M AAGVP VPG G +D + ++GYP+IIK GGGG+GMR+V +D S Sbjct: 125 AMIAAGVPTVPGSDGPLPEDEETALGIGREVGYPVIIKAAGGGGGRGMRVVHKEEDLISS 184 Query: 217 FLGAQREAAASFGVNTILLEKYITRPRHIEVQIFGDKHGNVLHLYERDCSVQRRHQKIIE 276 + EA A+FG + LEK++T PRH+EVQ+ D G+ +HL +RDCS+QRRHQK++E Sbjct: 185 AKLTRSEAGAAFGNPMVYLEKFLTNPRHVEVQVLSDGQGHAIHLGDRDCSLQRRHQKVLE 244 Query: 277 EAPAPNISEKFRANLGQAAVSAARAVGYYNAGTVEFIVDTESDQFYFMEMNTRLQVEHPV 336 EAPAP I EK RA + V A +GY AGT EF+ E+ FYF+EMNTR+QVEHPV Sbjct: 245 EAPAPGIDEKARAEVLARCVKACIDIGYRGAGTFEFLY--ENGHFYFIEMNTRVQVEHPV 302 Query: 337 TEMIVGQDLVEWQIRVANGEPLPLSQSEVPMSGHAFEARIYAENVPKGFLPATGVLNHYR 396 +EM+ G D+V+ + +A G L +Q +V + GHA E RI AE+ PK F+P+ G + H+ Sbjct: 303 SEMVTGIDIVKEMLSIAAGNKLSYTQDDVVIRGHALECRINAED-PKTFMPSPGTVKHFH 361 Query: 397 PVAVSPSVRVETGVEQGDTVSMHYDPMIAKLVVWGGNRGEALVKLKDCLSNFQVAGVPTN 456 VRV++ + G V +YD +I KL+ +G R EA+ ++++ L V G+ TN Sbjct: 362 APG-GNGVRVDSHLYSGYAVPPNYDSLIGKLITYGATRDEAMARMRNALDEIVVDGIKTN 420 Query: 457 INFLQKLASHKEFAVGNVETHFIEH 481 I + L F G V H++EH Sbjct: 421 IPLHRDLVRDAGFCEGGVNIHYLEH 445 Lambda K H 0.316 0.132 0.386 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 880 Number of extensions: 39 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 734 Length of database: 452 Length adjustment: 36 Effective length of query: 698 Effective length of database: 416 Effective search space: 290368 Effective search space used: 290368 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory